The idea has been raised before and musing on my way back from work made me consider the viability of re-enforcing the character of each org by linking reputation to pvp in addition to the missions etc. My problem is finding a fair symmetry to the award, so it remains a work in progress.
The basis for the distinction is the presence of the truce and the broad definition of Zion=citizen, Machine=authority, Merov=underworld with a kick to the appropriate aggression factors involved.
For example
If you are Zion you would lose 1 rep point for every x cq's gained from machines, you would gain 1 rep for every 2x cq's gained from Merovs.
iF you are Machine you would lose 1 for every 2x cq's taken from Zion, you would gain 1 rep for every x cq's gained from merovs
If your are Merov you gain 1 rep for every 4x cq's
I was figuring x=8 as a rule fo thumb.
An alternate approach might be to have a terminal screen in game (a la CoH) which can be iterrogated to list the online players for each org with a rep over 110 and effectively make reputation point only 'gainable' when the cq comes from one of them...in this way you become a target by your status relative to your organisation etc and it gives a degree of meaning to the resulting pvp.